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*
>
> _______________________________________________
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> 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 - 06:00:02 PST
