What version of GNU compilers are you using? What are the options you
are passing to configure? Although in your initial post you say you
are trying to compile with gcc, your error message makes it look like
you're really using clang.
-Dan
On Thu, Mar 9, 2017 at 8:45 AM, Tom Dreyfus <tom.dreyfus.inria.fr> wrote:
> Hi,
>
> thank you for your answer.
>
> I am using the last release version of AmberTools available on the
> official website (AmberTools16)
>
> I need parmed and openmm for computing the potential energy of a small
> peptide (succeedly installed). While parmed alone allows me to load the
> force fields parameters, computing the potential energy of a molecule
> fails because the topology of the molecule is not loaded.
>
> It seems that the only way is to load the topology from the prmtop file,
> this is why I need to compile AmberTools, or at least the leap
> executables for building such file.
>
>
> Tom.
>
> On 03/09/2017 02:33 PM, Daniel Roe wrote:
>> Hi,
>>
>> Which version of AmberTools are you using?
>>
>> Also, if all you need is parmed you can always get it straight from
>> GitHub: https://github.com/ParmEd/ParmEd
>>
>> -Dan
>>
>> On Thu, Mar 9, 2017 at 8:04 AM, Tom Dreyfus <tom.dreyfus.inria.fr> wrote:
>>>> Dear Amber developpers,
>>>>
>>>> We are very much interested in using the Amber force field. Of
>>>> particular interest is the Python library Parmed
>>>> (https://parmed.github.io/ParmEd/html/amber.html), as it allows
>>>> accessing the potential energy terms one by one.
>>>>
>>>> We need to generate the prmtop files, which requires the AmberTools suite.
>>>>
>>>> We have followed the steps described in the installation
>>>> documentation, but unfortunately did not succeed to build the tools. I
>>>> have got the following errors i am stuck with (see below).
>>>>
>>>> I am using Fedora 23 and try to compile using gcc.
>>>>
>>>> Can you please guide us on how to compile the tools ?
>>>>
>>>> Thank you for your attention.
>>>>
>>>> Tom.
>>>>
>>>> *In file included from pdb_type.cpp:29:**
>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:100:3:
>>>> error: conflicting types for 'memchr'**
>>>> ** memchr(void* __s, int __c, size_t __n)**
>>>> ** ^**
>>>> **/usr/include/string.h:92:14: note: previous declaration is here**
>>>> **extern void *memchr (const void *__s, int __c, size_t __n)**
>>>> ** ^**
>>>> **In file included from pdb_type.cpp:29:**
>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:104:3:
>>>> error: conflicting types for 'strchr'**
>>>> ** strchr(char* __s, int __n)**
>>>> ** ^**
>>>> **/usr/include/string.h:231:14: note: previous declaration is here**
>>>> **extern char *strchr (const char *__s, int __c)**
>>>> ** ^**
>>>> **In file included from pdb_type.cpp:29:**
>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:108:3:
>>>> error: conflicting types for 'strpbrk'**
>>>> ** strpbrk(char* __s1, const char* __s2)**
>>>> ** ^**
>>>> **/usr/include/string.h:310:14: note: previous declaration is here**
>>>> **extern char *strpbrk (const char *__s, const char *__accept)**
>>>> ** ^**
>>>> **In file included from pdb_type.cpp:29:**
>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:112:3:
>>>> error: conflicting types for 'strrchr'**
>>>> ** strrchr(char* __s, int __n)**
>>>> ** ^**
>>>> **/usr/include/string.h:258:14: note: previous declaration is here**
>>>> **extern char *strrchr (const char *__s, int __c)**
>>>> ** ^**
>>>> **In file included from pdb_type.cpp:29:**
>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:116:3:
>>>> error: conflicting types for 'strstr'**
>>>> ** strstr(char* __s1, const char* __s2)**
>>>> ** ^**
>>>> **/usr/include/string.h:337:14: note: previous declaration is here**
>>>> **extern char *strstr (const char *__haystack, const char *__needle)**
>>>> ** ^**
>>>> **5 errors generated.*
>>>>
>>>> AND
>>>>
>>>> */usr/bin/clang++ -o reduce GraphToHoldScores.o reduce.o CTab.o
>>>> ElementInfo.o StdResH.o ResBlk.o AtomConn.o AtomPositions.o DotSph.o
>>>> Mover.o RotMethyl.o RotAromMethyl.o RotDonor.o FlipMemo.o CliqueList.o
>>>> AtomDescr.o PDBrec.o MoveableNode.o hybrid_36_c.o -L../libpdb -lpdb++
>>>> -L../toolclasses -ltoolclasses -lm **
>>>> **/usr/bin/ld: cannot find -lpdb++**
>>>> **clang: error: linker command failed with exit code 1 (use -v to see
>>>> invocation)**
>>>> **Makefile:41: recipe for target 'reduce' failed*
>>> On 03/09/2017 02:02 PM, Tom Dreyfus wrote:
>>>>> Dear Amber developpers,
>>>>>
>>>>> We are very much interested in using the Amber force field. Of
>>>>> particular interest is the Python library Parmed
>>>>> (https://parmed.github.io/ParmEd/html/amber.html), as it allows
>>>>> accessing the potential energy terms one by one.
>>>>>
>>>>> We need to generate the prmtop files, which requires the AmberTools
>>>>> suite.
>>>>>
>>>>> We have followed the steps described in the installation
>>>>> documentation, but unfortunately did not succeed to build the tools.
>>>>> I have got the following errors i am stuck with (see below).
>>>>>
>>>>> I am using Fedora 23 and try to compile using gcc.
>>>>>
>>>>> Can you please guide us on how to compile the tools ?
>>>>>
>>>>> Thank you for your attention.
>>>>>
>>>>> Tom.
>>>>>
>>>>> *In file included from pdb_type.cpp:29:**
>>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:100:3:
>>>>> error: conflicting types for 'memchr'**
>>>>> ** memchr(void* __s, int __c, size_t __n)**
>>>>> ** ^**
>>>>> **/usr/include/string.h:92:14: note: previous declaration is here**
>>>>> **extern void *memchr (const void *__s, int __c, size_t __n)**
>>>>> ** ^**
>>>>> **In file included from pdb_type.cpp:29:**
>>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:104:3:
>>>>> error: conflicting types for 'strchr'**
>>>>> ** strchr(char* __s, int __n)**
>>>>> ** ^**
>>>>> **/usr/include/string.h:231:14: note: previous declaration is here**
>>>>> **extern char *strchr (const char *__s, int __c)**
>>>>> ** ^**
>>>>> **In file included from pdb_type.cpp:29:**
>>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:108:3:
>>>>> error: conflicting types for 'strpbrk'**
>>>>> ** strpbrk(char* __s1, const char* __s2)**
>>>>> ** ^**
>>>>> **/usr/include/string.h:310:14: note: previous declaration is here**
>>>>> **extern char *strpbrk (const char *__s, const char *__accept)**
>>>>> ** ^**
>>>>> **In file included from pdb_type.cpp:29:**
>>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:112:3:
>>>>> error: conflicting types for 'strrchr'**
>>>>> ** strrchr(char* __s, int __n)**
>>>>> ** ^**
>>>>> **/usr/include/string.h:258:14: note: previous declaration is here**
>>>>> **extern char *strrchr (const char *__s, int __c)**
>>>>> ** ^**
>>>>> **In file included from pdb_type.cpp:29:**
>>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:116:3:
>>>>> error: conflicting types for 'strstr'**
>>>>> ** strstr(char* __s1, const char* __s2)**
>>>>> ** ^**
>>>>> **/usr/include/string.h:337:14: note: previous declaration is here**
>>>>> **extern char *strstr (const char *__haystack, const char *__needle)**
>>>>> ** ^**
>>>>> **5 errors generated.*
>>>>>
>>>>> AND
>>>>>
>>>>> */usr/bin/clang++ -o reduce GraphToHoldScores.o reduce.o CTab.o
>>>>> ElementInfo.o StdResH.o ResBlk.o AtomConn.o AtomPositions.o DotSph.o
>>>>> Mover.o RotMethyl.o RotAromMethyl.o RotDonor.o FlipMemo.o
>>>>> CliqueList.o AtomDescr.o PDBrec.o MoveableNode.o hybrid_36_c.o
>>>>> -L../libpdb -lpdb++ -L../toolclasses -ltoolclasses -lm **
>>>>> **/usr/bin/ld: cannot find -lpdb++**
>>>>> **clang: error: linker command failed with exit code 1 (use -v to see
>>>>> invocation)**
>>>>> **Makefile:41: recipe for target 'reduce' failed*
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Mar 09 2017 - 06:00:04 PST
